title: Transcriptomic analysis of genes modulated by cyclo(L-phenylalanine-L-proline) in Vibrio vulnificus.
abstract: Diketopiperazine is produced by various organisms, including bacteria, fungi, and animals, and has been suggested as a novel signal molecule involved in the modulation of genes with various biological functions. Vibrio vulnificus, which causes septicemia in humans, produces cyclo(L-phenylalanine-L-proline) (cFP). To understand the biological roles of cFP, the effect of the compound on the expression of the total mRNA in V. vulnificus was assessed by nextgeneration sequencing. Based on the transcriptomic analysis, we classified the cFP-regulated genes into functional categories and clustered them according to the expression patterns resulted from treatment with cFP. From a total of 4,673 genes, excepting the genes encoding tRNA in V. vulnificus, 356 genes were up-regulated and 602 genes were down-regulated with an RPKM (reads per kilobase per million) value above 3. The genes most highly induced by cFP comprised those associated with the transport and metabolism of inorganic molecules, particularly iron. The genes negatively regulated by cFP included those associated with energy production and conversion, as well as carbohydrate metabolism. Noticeably, numerous genes related with biofilm formation were modulated by cFP. We demonstrated that cFP interferes significantly with the biofilm formation of V. vulnificus.
authors.affiliation: Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Baekbeom-Ro 35, Mapo-Gu, Seoul 121-742, Republic of Korea.
authors.forename: In Hwang
authors.initials: IH
authors.lastname: Kim
authors.forename: Jee-Soo
authors.initials: JS
authors.lastname: Son
authors.forename: Yancheng
authors.initials: Y
authors.lastname: Wen
authors.forename: Sang-Min
authors.initials: SM
authors.lastname: Jeong
authors.forename: Ga-Young
authors.initials: GY
authors.lastname: Min
authors.forename: Na-Young
authors.initials: NY
authors.lastname: Park
authors.forename: Keun-Woo
authors.initials: KW
authors.lastname: Lee
authors.forename: Yong-Joon
authors.initials: YJ
authors.lastname: Cho
authors.forename: Jongsik
authors.initials: J
authors.lastname: Chun
authors.forename: Kun-Soo
authors.initials: KS
authors.lastname: Kim
mesh_terms: D004151:Dipeptides / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D059014:High-Throughput Nucleotide Sequencing; D010456:Peptides, Cyclic / Q000378:metabolism*; D041261:Vibrio vulnificus / Q000187:drug effects* / Q000235:genetics*
chemical_list: D004151:Dipeptides; D010456:Peptides, Cyclic; C118540:cyclo(phenylalanyl-prolyl)